data_20121 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Tubulysin conformation bound to tubulin ; _BMRB_accession_number 20121 _BMRB_flat_file_name bmr20121.str _Entry_type original _Submission_date 2010-02-03 _Accession_date 2010-02-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kubicek Karel . . 2 Grimm Steffen K. . 3 Orts Julien . . 4 Sasse Florenz . . 5 Carlomagno Teresa . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 structure_coordinate_set 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 52 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-23 update BMRB 'PDBj annotated the coordinate file' 2010-08-13 update BMRB 'Complete entry citation' 2010-07-26 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'The tubulin-bound structure of the antimitotic drug tubulysin.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20496362 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kubicek Karel . . 2 Grimm 'S. Kaspar' . . 3 Orts Julien . . 4 Sasse Florenz . . 5 Carlomagno Teresa . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_name_full 'Angewandte Chemie (International ed. in English)' _Journal_volume 49 _Journal_issue 28 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4809 _Page_last 4812 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name tubulysin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label tubulysin $tubulysin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_tubulysin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common tubulysin _Molecular_mass 841 _Mol_thiol_state 'not available' loop_ _Biological_function 'Inhibiting tubulin polymerization' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence XIXX loop_ _Residue_seq_code _Residue_label 1 T23 2 ILE 3 TUV 4 TUT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_T23 _Saveframe_category polymer_residue _Mol_type 'RNA linking' _Name_common 2'-O-METHYL-3'-METHYL-3'-DEOXY-ARABINOFURANOSYL-THYMINE-5'-PHOSPHATE _BMRB_code . _PDB_code T23 _Standard_residue_derivative . _Molecular_mass 350.262 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 16:20:55 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? O5' O5' O . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C5M C5M C . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C2M C2M C . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? C3' C3' C . 0 . ? C3M C3M C . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? H6 H6 H . 0 . ? H3 H3 H . 0 . ? H5A1 H5A1 H . 0 . ? H5A2 H5A2 H . 0 . ? H5A3 H5A3 H . 0 . ? H2' H2' H . 0 . ? H2M1 H2M1 H . 0 . ? H2M2 H2M2 H . 0 . ? H2M3 H2M3 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H3' H3' H . 0 . ? H3M1 H3M1 H . 0 . ? H3M2 H3M2 H . 0 . ? H3M3 H3M3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING OP3 HOP3 ? ? SING O5' C5' ? ? SING N1 C6 ? ? SING N1 C2 ? ? SING N1 C1' ? ? DOUB C6 C5 ? ? SING C6 H6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? SING C5M H5A1 ? ? SING C5M H5A2 ? ? SING C5M H5A3 ? ? SING C2' O2' ? ? SING C2' C1' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING O2' C2M ? ? SING C2M H2M1 ? ? SING C2M H2M2 ? ? SING C2M H2M3 ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' H1' ? ? SING C3' C3M ? ? SING C3' H3' ? ? SING C3M H3M1 ? ? SING C3M H3M2 ? ? SING C3M H3M3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $tubulysin . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $tubulysin 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $tubulysin 0.5 mM 'natural abundance' tubulin 0.01 mM 'natural abundance' 'sodium phosphate' 1.5 mM 'natural abundance' 'calcium phosphate' 1.5 mM 'natural abundance' H2O 95 % 'natural abundance' DMSO 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.31 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.0 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name tubulysin _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 T23 HA H 3.647 . 1 2 1 1 T23 HB1 H 2.106 . 1 3 1 1 T23 HB2 H 1.734 . 1 4 1 1 T23 HD1 H 1.695 . 2 5 1 1 T23 HE1 H 3.418 . 1 6 1 1 T23 HE2 H 2.936 . 1 7 1 1 T23 HG1 H 1.869 . 1 8 1 1 T23 HG2 H 1.503 . 1 9 1 1 T23 HZ1 H 2.620 . 2 10 1 1 T23 HZ2 H 2.620 . 2 11 1 1 T23 HZ3 H 2.620 . 2 12 2 2 ILE HA H 4.577 . 1 13 2 2 ILE HB H 1.965 . 1 14 1 2 ILE HD1 H 0.848 . 2 15 2 2 ILE HG12 H 1.185 . 1 16 2 2 ILE HG13 H 1.167 . 1 17 1 2 ILE HG2 H 0.934 . 2 18 3 3 TUV HA H 4.343 . 1 19 3 3 TUV HB H 1.853 . 1 20 3 3 TUV HB2 H 8.069 . 1 21 3 3 TUV HD11 H 5.337 . 1 22 3 3 TUV HD12 H 6.130 . 1 23 3 3 TUV HD21 H 2.686 . 1 24 3 3 TUV HD22 H 2.603 . 1 25 3 3 TUV HE2 H 5.823 . 1 26 3 3 TUV HG11 H 0.709 . 2 27 3 3 TUV HG12 H 0.709 . 2 28 3 3 TUV HG13 H 0.709 . 2 29 3 3 TUV HG21 H 1.027 . 2 30 3 3 TUV HG22 H 1.027 . 2 31 3 3 TUV HG23 H 1.027 . 2 32 3 3 TUV HK11 H 2.089 . 1 33 3 3 TUV HK12 H 2.006 . 1 34 3 3 TUV HL1 H 1.732 . 1 35 3 3 TUV HL21 H 2.168 . 2 36 3 3 TUV HL22 H 2.168 . 2 37 3 3 TUV HL23 H 2.168 . 2 38 3 3 TUV HM1 H 0.682 . 2 39 3 3 TUV HM2 H 0.682 . 2 40 3 3 TUV HM3 H 0.682 . 2 41 3 3 TUV HN1 H 0.715 . 2 42 3 3 TUV HN2 H 0.715 . 2 43 3 3 TUV HN3 H 0.715 . 2 44 4 4 TUT HA H 4.149 . 1 45 4 4 TUT HB1 H 2.930 . 1 46 4 4 TUT HB2 H 2.687 . 1 47 4 4 TUT HE1 H 7.099 . 3 48 4 4 TUT HE2 H 6.720 . 3 49 4 4 TUT HI1 H 2.375 . 1 50 4 4 TUT HM1 H 1.082 . 1 51 4 4 TUT HQ1 H 1.588 . 1 52 4 4 TUT HQ2 H 1.932 . 1 stop_ save_